While I understand that some changes in an entire population can occur over long periods of time (especially if a population becomes isolated from others of their same kind), I don't subscribe to the belief that these slight changes over millions of years eventually accumulate into the birth a new kind of organism altogether. Yes, variations in organisms is directly observable. However, common ancestry between diverse types of organisms must be assumed. Similarities in organisms only strongly imply common ancestry when coupled with the presupposition of ontological naturalism.
I say all this to get at the root problem here. Mutations are the Darwinianists only hope of generating new genetic information.
Since mutations occur in individuals that are already adapted to their environment, virtually all mutations represent corruptions to the genetic information. Mutations, even if they were deemed beneficial, actually represent a loss of information because their original sequence has been damaged. Any gain is offset by loss.
Again, since natural selection is the primary mechanism that promotes changes in the number of particular traits in a population, we run into the same problem. Natural selection is basically a weeding out process. It does not create anything new, it only selects from what is present already and does so by a process of elimination.
Therefore, the major factors that influence the frequency of genes and traits in a population do so primarily through negative effects - the loss of genetic information and a decrease in the variation within a population.
My contention (stemming from a plain reading of Genesis) is that God supernaturally created mature organisms (of various specific kinds) and included tremendous genetic diversity in these from the beginning. As such, I hold that rather than new types organisms coming into existence over time, we are actually observing, for the most part, a loss and extinction of types of organisms.
I see no problem with Adam and Eve being the sole ancestors of the entire human population.